[gmx-users] Problem in setup energy minimization step(grompp)

[Justin A. Lemkul]

X Rules wrote:
> 
> 
>  > Date: Mon, 26 Jul 2010 07:26:04 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] Problem in setup energy minimization 
> step(grompp)
>  >
>  >
>  >
>  > X Rules wrote:
>  > > Precisely,
>  > >
>  > > open your xyz.top file and search for #include "spc.itp" and replace
>  > > this line with #include "tip4p.itp"
>  > >
>  > > and you will be done with.
>  > >
>  >
>  > Not if the coordinates present are for a three-point water model, in 
> which case
>  > the same error is occurring. If you're switching models like this, 
> you have to
>  > re-build the system.
> 
> agreed, but I build my system entirely for tip4p, i.e adding tip4p using 
> genbox and still my top file contains spc.itp instead of tip4p.itp 
> (possible bug?? in 4.0.5 alteast).
> 

There is no bug.  The default water model written to the topology is spc.itp, 
but this can be chosen when running pdb2gmx with the -water flag.  The mechanism 
for choosing water models will be completely different in the upcoming version 
of GROMACS, such that the choice will be completely user-dependent.

-Justin

>  >
>  > -Justin
>  >
>  > >
>  > >
>  > > > Date: Mon, 26 Jul 2010 07:00:57 -0400
>  > > > From: jalemkul at vt.edu
>  > > > To: gmx-users at gromacs.org
>  > > > Subject: Re: [gmx-users] Problem in setup energy minimization
>  > > step(grompp)
>  > > >
>  > > >
>  > > >
>  > > > bipin.singh at research.iiit.ac.in wrote:
>  > > > >
>  > > > > Hi all,
>  > > > > I am facing a problem when i tried the TIP4P water model
>  > > > > for the set up of energy minimization using grompp.
>  > > > > This error did'nt occur while using the spce model.
>  > > > >
>  > > > > Fatal error:
>  > > > > number of coordinates in coordinate file (1.pdb, 31975)
>  > > > > does not match topology (1.top, 24795)
>  > > > > Please help me to rectify this problem.
>  > > > >
>  > > >
>  > > > So all you did was change the water model? That would certainly
>  > > explain it,
>  > > > since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise:
>  > > >
>  > > >
>  > > 
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>  > > >
>  > > > -Justin
>  > > >
>  > > > > Thanks
>  > > > > Bipin
>  > > >
>  > > > --
>  > > > ========================================
>  > > >
>  > > > Justin A. Lemkul
>  > > > Ph.D. Candidate
>  > > > ICTAS Doctoral Scholar
>  > > > MILES-IGERT Trainee
>  > > > Department of Biochemistry
>  > > > Virginia Tech
>  > > > Blacksburg, VA
>  > > > jalemkul[at]vt.edu | (540) 231-9080
>  > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  > > >
>  > > > ========================================
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>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================